Microbiology Metabolism & Catabolism Review

Comprehensive vocabulary flashcards covering microbial metabolism, thermodynamic laws, redox reactions, enzyme kinetics, and major catabolic/anabolic pathways based on lecture objectives.

Metabolism

The organized network of enzyme- or ribozyme-catalyzed pathways in a cell that obey thermodynamics and regulate energy flow and nutrient utilization.

Chemical work

A type of cellular work involving the biosynthesis of complex macromolecules.

Transport work

A type of cellular work involving nutrient uptake, waste export, and maintaining ion balance.

Mechanical work

A type of cellular work involving motility through flagella, cytoskeletal movement, or cell division.

First Law of Thermodynamics

Energy is conserved; it cannot be created or destroyed, only transformed.

Second Law of Thermodynamics

Spontaneous processes result in an increase in overall entropy; cells maintain internal order by coupling reactions to exergonic processes that increase entropy elsewhere.

Gibbs Free Energy Equation

$\Delta G = \Delta H - T\Delta S$; used to predict the spontaneity of a reaction where a negative $\Delta G$ indicates an exergonic process.

Standard conditions equation for Keq

$\Delta G^{\circ\prime} = -2.303 RT \log K_{eq}$; connects thermodynamics to the equilibrium position and driving force at pH 7.

Exergonic

A reaction with a negative $\Delta G^{\circ\prime}$ that is spontaneous at standard conditions.

Endergonic

A reaction with a positive $\Delta G^{\circ\prime}$ that requires energy coupling to proceed.

ATP Structure

Consists of adenine (nitrogenous base), ribose (sugar), and a chain of three phosphates (alpha, beta, gamma) held by two high-energy phosphoanhydride bonds.

$\Delta G^{\circ\prime}$ of ATP hydrolysis

Approximately $-7.3\,kcal/mol$.

Phosphate transfer potential

A ranking of molecules by their ability to donate phosphate groups; PEP > ATP > G6P.

Oxidation

The loss of electrons from a molecule.

Reduction

The gain of electrons by a molecule.

Standard reduction potential ($E_0^{\prime}$)

A measure of the tendency of a donor to lose electrons; more negative values indicate better electron donors, while more positive values indicate better acceptors.

Equation linking $\Delta G^{\circ\prime}$ to $\Delta E_0^{\prime}$

$\Delta G^{\circ\prime} = - n F \Delta E_0^{\prime}$, where n is the number of electrons and F is Faraday's constant.

Quinones (CoQ/UQ, MQ)

Lipid-soluble components of the ETC that carry both electrons ($e^-$) and protons ($H^+$).

Cytochromes

ETC carriers containing heme that carry only electrons ($e^-$).

Iron-sulfur proteins (ferredoxin)

ETC carriers that carry only electrons ($e^-$).

Apoenzyme

The protein-only component of an enzyme.

Holoenzyme

A complete, active enzyme consisting of an apoenzyme plus its required cofactor.

Prosthetic group

A cofactor that is tightly or covalently bound to the apoenzyme, such as FAD.

Coenzyme

A diffusible, loosely bound organic cofactor, such as NAD+.

Competitive Inhibition

Inhibitor competes at the active site; it increases the apparent $K_m$ but leaves $V_{max}$ unchanged.

Noncompetitive Inhibition

Inhibitor binds to an allosteric site; it lowers the $V_{max}$ but $K_m$ often remains unchanged.

Ribozymes

Catalytic RNA molecules, such as the peptidyl transferase center in the ribosome.

Metabolic Channeling

The spatial organization of enzymes and metabolites in compartments (e.g., carboxysomes) to regulate pathway flux.

Feedback inhibition

Also called end-product inhibition; the final product of a pathway inhibits the pacemaker enzyme at the beginning.

Photolithoautotroph

An organism that uses light for energy, inorganic donors for electrons, and $CO_2$ as its carbon source.

Chemoorganoheterotroph

An organism that derives carbon, energy, and electrons from organic compounds.

Embden–Meyerhof Pathway (EMP)

The classical glycolysis pathway that nets $2 \text{ ATP}$, $2 \text{ NADH}$, and $2 \text{ pyruvate}$ per glucose.

Entner–Doudoroff Pathway (ED)

An alternative glucose catabolism pathway found in some Gram-bacteria that nets $1 \text{ ATP}$, $1 \text{ NADPH}$, and $1 \text{ NADH}$.

Pentose Phosphate Pathway (PPP)

A pathway that produces NADPH for biosynthesis and ribose-5-P for nucleotide synthesis.

Pyruvate Dehydrogenase Complex (PDH)

A multienzyme complex (E1-E2-E3) that performs oxidative decarboxylation to turn pyruvate into acetyl-CoA, $CO_2$, and NADH.

TCA Cycle yields per Acetyl-CoA

$3 \text{ NADH}$, $1 \text{ FADH}_2$, $1 \text{ GTP}$, and $2 \text{ CO}_2$.

Chemiosmotic Hypothesis

The theory that ETC-driven proton pumping creates a proton motive force (PMF) used to drive ATP synthesis.

Proton Motive Force (PMF) formula

$\Delta p = \Delta \Psi + 59\,mV \cdot \Delta pH$.

Binding-change mechanism

The process where rotation of the F0 rotor in ATP synthase drives conformational changes in F1 (O, L, T states) to synthesize ATP.

Nitrification

The aerobic two-step oxidation of ammonia ($NH_3$) to nitrate ($NO_3^-$).

Denitrification

Anaerobic respiration using nitrate ($NO_3^-$) as a terminal electron acceptor, reducing it to $N_2$ gas.

Reverse Electron Flow

An energy-intensive process used by chemolithotrophs to generate NADPH when the electron donor has a more positive $E_0^{\prime}$ than NAD+/NADH.

Electron Bifurcation

A mechanism that splits an electron pair, sending one uphill (endergonic) and one downhill (exergonic) to enable unfavorable reductions.

Oxygenic Photosynthesis

Uses two photosystems and $H_2O$ as an electron donor to produce $O_2$, ATP, and NADPH.

Rhodopsin-based phototrophy

A system where a retinal protein acts as a light-driven proton pump to create PMF without an electron transport chain.

Anaplerotic reactions

Reactions that replenish TCA cycle intermediates, such as the glyoxylate cycle, which bypasses $CO_2$ loss steps.